Use these PATE functions to process the data from GCS
pate-rnd xmap-collector --include_file_str QC_Gamma \
--out_file_name gamma_qc.csv
Use this to import the data into JH from GCS
gsutil cp gs://inhouse-xmap-data/user_data_frames/gamma_qc.csv
/home/ddhillon/projects/beta-av-testing/data/raw/gamma_qc.csv
This is a one off quick check experiment to make sure everything looks ok
## New names:
## * `` -> ...1
There are two runs for panel 2 - why? this is because one of the QCs for the march 3rd run was switched and Jinesh and Wilson changed the platemap and re-ran the software
We will only use the 7th march data since it has the correct positioning
## # A tibble: 3 × 2
## file_name n
## <chr> <int>
## 1 20220303_QC_Gamma_Panel1_20220304_135209.csv 4608
## 2 20220303_QC_Gamma_Panel2_20220304_133848.csv 3072
## 3 20220307_QC_Gamma_Panel2_20220307_141423.csv 3072
We take the curve fit by gamma, and then interpolate the beta standards and check the concentrations. We will then use these interpolated concentrations to see what the % recovery is, and whether it is within the expected interval we expect it to be.
## New names:
## * `` -> ...1
## # A tibble: 42 × 3
## xponent_id assay n
## <chr> <chr> <int>
## 1 Standard1 CEA 231
## 2 Standard1 FLT3L 261
## 3 Standard1 IL-1 R2 258
## 4 Standard1 IL-8 255
## 5 Standard1 MUC-16 259
## 6 Standard1 TNC 232
## 7 Standard1 WFDC2 231
## 8 Standard2 CEA 236
## 9 Standard2 FLT3L 262
## 10 Standard2 IL-1 R2 259
## # … with 32 more rows
## `summarise()` has grouped output by 'xponent_id'. You
## can override using the `.groups` argument.
## # A tibble: 42 × 3
## xponent_id assay n
## <chr> <chr> <int>
## 1 Standard1 CEA 1
## 2 Standard1 FLT3L 1
## 3 Standard1 IL-1 R2 1
## 4 Standard1 IL-8 1
## 5 Standard1 MUC-16 1
## 6 Standard1 TNC 1
## 7 Standard1 WFDC2 1
## 8 Standard2 CEA 1
## 9 Standard2 FLT3L 1
## 10 Standard2 IL-1 R2 1
## # … with 32 more rows
Now we take the beta_interpolated data and merge it with our historical data
gsutil cp /home/ddhillon/projects/beta-av-testing/notebooks/gamma-lot-qc/outputs/exp-01.html gs://freenome-user-data-ddhillon/outputs/